Using the MGI BioMart Datasets
More Help

This help document answers the following questions:

What is a BioMart?

BioMart is a query-oriented data management and integration system that performs like a batch query. The system can be applied to a single or to multiple databases. It provides fast, powerful, and complex queries to an individual database, federations (connections) with other databases, and ongoing enhancements. BioMart can be used to convert one or more data sources (flat files or a relational databases) into data marts that are accessible either with a web browser or with Perl, Java and webservice APIs (Application Program Interfaces).

BioMart is a joint development of the Ontario Institute for Cancer Research (OICR) and the European Bioinformatics Institute (EBI).


What are some of the advantages of using MGI BioMart?

BioMart provides an efficient solution to issues such as:

BioMart provides one generic interface, one resource, with no need for a custom SQL/web service/API. You can import data, reiterate and refine queries on one page, and integrate your data with other datasets that MGI BioMart hosts (e.g. Ensembl, VEGA, RGD) and export results, all without cutting and pasting. You can also combine filters and attributes to fully annotate your dataset with a remote one, all without a custom SQL, web service, or API.


What databases are available through the MGI BioMart?

MGI BioMart provides access to 3 databases, composed of datasets.

Databases currently available for access are named:


What datasets are available in the MGI BioMart?

MGI Biomart datasets:

A dataset is a collection of data tables that follow a given naming convention. Each column in the table represents a variable. Each row corresponds to a member of the dataset. Examples are

MGI BioMart filters - restrict a query by selecting:

MGI BioMart attributes - determine the data columns displayed in the query results:


How do I use MGI BioMart?

You use MGI BioMart to:

To do this:

Click and then select options from the right and left panes of the user interface:

See also Are there additional tips for using MGI BioMart?


Can I tell in advance the size of the dataset that a query returns?



What is the function of filters?

MGI BioMart uses the concept of filters for narrowing or expanding a query. Initially, you may wish to query the entire set of genes and genome features in MGI, but you can also query a smaller, more limited set (for example, by importing a list of IDs or symbols or selecting a specific region of a chromosome) using the filters. Below are expanded images of all MGI BioMart Genes & Genome Features and Gene Expression Data filter categories.

select filters
select gxd filters


What is the function of attributes?

BioMart identifies the dataset information to add to your query results as attributes. Below are expanded images of MGI BioMart Genes & Genome Features and Gene Expression data (GXD) attribute categories.

select filters
select gxd attributes

Below are the attribute names to use when querying for Genes & Genome Features data followed by examples of what MGI BioMart returns.

 Attribute NameExamples
Feature SymbolActb
Feature Nameactin, beta
Feature Typeprotein coding gene
Feature SynonymsActx
Mouse Entrez gene ID11461
Mouse Ensembl gene IDENSMUSG00000029580
Mouse VEGA gene IDOTTMUSG00000015100
GO ID (gene ontology identifier)GO:0006916
GO termprotein kinase binding
Genome Location
Chromosome1 thru 19, X, Y, XY, MT, UN
Start Coordinate (bp)143665420
End Coordinate (bp)143668404
strand+ or -
MGI allele IDMGI:2180089
Allele SymbolActbtm1bhr
Allele Nametargeted mutation 1, Richard R. Behringer
Allele TypeTargeted (knock-out)
Phenotype IDMP:0003984
Phenotype Termembryonic growth retardation
Human SymbolActb
Human Entrez Gene ID81822
Rat SymbolACTB
Rat Entrez Gene ID60

Below are the attribute names to use when querying for gene expression data followed by examples of what MGI BioMart returns.

GXD AttributesAttribute NameExamples
GeneGene SymbolShh
MGI Gene IDMGI:98297
AssayMGI Assay IDMGI:1275014
Assay TypeRNA in situ
MGI Probe IDMGI:1194645
MGI Antibody IDMGI:3053439
Genotype of SpecimenMutant Allele(s)Shhtm2Amc
Stage And Anatomical StructureAgeE18.5
Theiler StageTS26
Anatomical StructureCerebellum
Expression ResultsLevelTrace
In Situ AssayPatternRegionally restricted
Reference IDsJ NumberJ:108509
PubMed ID16571630


How can I use BioMart to search for specific genome feature types?

The image below depicts the results of this search.


How can I use BioMart to search for gene expression data?

As an example, here is how you can find In situ reporter (knock-in) assays that show expression in diencephalon:

The image below depicts a portion of the results of this search.

gxd results


My query returned no results. Why?


Are there data that MGI BioMart does not currently search for/find?

Yes. The MGI BioMart does not yet contain all MGI data. For example, for the Genes & Genome Features dataset, it does not recognize secondary marker IDs. Secondary IDs are neither counted (e.g. when you click Count) nor do they appear when you click Results.

MGI gene detail pages list secondary IDs in the Other accession IDs section at the bottom. For example, the Kit gene detail page lists MGD-MRK-11588, MGD-MRK-14609, MGD-MRK-15420, MGD-MRK-1672, MGD-MRK-9743, MGI:3530304, MGI:3530312, MGI:3530319. None of these are returned if/when you include Kit in the Feature Symbol list of an MGI BioMart query.


How can I change the sort order in my query results?

The order in which items appear under Attributes (left panel) is the order of the columns in which the query results appear. As an example, for Genes & Genome Feature results, by default, Feature Symbol and Feature Name are the first two columns. To change the order:

  1. Click Attributes.
  2. Click to open attribute lists in the right panel (e.g. Features, Genome Location, Alleles, Orthologs).
  3. Select an item (e.g. MGI ID, Feature Type, etc.) from an attribute list. When you do so, the item appears beneath Attributes in the left-hand panel.
  4. Deselect any attribute that you do not want to appear as a column in your results.
  5. Continue selecting/deselecting attributes until they appear in the desired column order (on the left).
  6. Click Results again.
  7. Repeat until satisfied with the result.


What can I do on a result page?


Are there any additional tips for using MGI BioMart?

Yes. Be aware that:

MGI BioMart does allow you to:


Where can I find additional BioMart information?

The BioMart Project website has additional information.